Genetics of one-carbon metabolism in sheep in relation to productivity, fertility and health

这个项目的重点是羊的健康、生产力和福利。我们将集中在新陈代谢的方面，影响终身健康和福祉。具体来说，我们将研究代谢的一个关键方面，即一碳（1C）代谢。这很重要，因为它影响细胞中的许多关键过程，包括DNA合成、DNA甲基化和细胞增殖。它通过传递甲基来实现这一点，甲基是这些生化反应的核心。参与这些途径的代谢物，如胆碱、蛋氨酸、叶酸和维生素B12的缺乏，对动物的发育和健康有不利影响。例如，缺乏维生素B12和/或叶酸会影响生育能力和胎儿发育，并导致成年动物和人类生长不良、血管疾病和代谢综合征。1C代谢途径复杂，受多种基因影响。我们假设这些基因的突变会影响1C代谢和动物对微量营养素缺乏的脆弱性。在这项研究中，我们将识别这些突变，确定它们的功能意义（即它们的作用和重要性），测试它们对饲喂不同饮食的动物的影响，并找到利用这些信息改善农场动物福利的方法。首先，我们将确定直接影响1C代谢的约40个基因的突变（即单核苷酸多态性或snp），以及涉及能量代谢、细胞增殖、DNA合成和DNA甲基化的非常密切相关的途径。为了在绵羊中实现这一点，我们将创建我们自己的序列数据。我们估计我们将通过这些方法识别2000-4000个snp。然后，我们将对从当地屠宰场屠宰的约300只羊身上收集的肝脏样本进行大规模研究。我们将对每个样本进行基因分型（以确定存在哪些snp），测量基因表达，并对1C代谢相关的所有代谢物进行综合分析。对这些数据的解释将告诉我们SNP的功能以及这些SNP如何影响1C代谢的途径。为了实现这一目标，我们将整理所需的信息，并利用我们对这些基因组的了解，结合复杂的生物信息学分析，确定对1C代谢影响最大的snp子集。我们期望在这些基因中鉴定出大约100个具有重要功能的snp。然后我们将构建一个“SNP芯片”；也就是说，一种同时对许多snp进行廉价基因分型的工具。该芯片将用于筛选几群绵羊，以确定24只“低风险”和24只“高风险”断奶羔羊，以及24只“低风险”和24只“高风险”繁殖母羊。然后，我们将在涉及对照和甲基缺乏饮食（即两种饮食的两种基因型）的单独研究中监测这些动物。对于断奶羔羊，我们将重点关注对生长、动物健康和肝脏代谢、胴体产量和组成的影响。对于繁殖母羊，我们也将关注动物健康和肝脏代谢，但将研究扩展到考虑早期（第16天）雄性和雌性胚胎中DNA化学修饰（即DNA甲基化）的影响。这项研究将为1C代谢的许多组成部分提供营养x基因相互作用的新见解，以及它们如何影响(a)羔羊的生产效率、健康和福利，以及(b)哺乳动物胚胎的早期发育影响生育能力和后代的长期健康和福祉。我们将能够利用这些信息来帮助培育具有更好1C代谢功能的动物（导致福利和生产力的永久改善）和/或改善动物的饮食。由于1C代谢也影响人类的发育和健康，我们的研究结果也将对生物医学研究有益，并增加羊作为这类研究的模式物种的效用。

This project is focussed on the health, productivity and welfare of sheep. We will concentrate on aspects of metabolism that affect lifelong health and wellbeing. Specifically, we will study a key aspect of metabolism referred to as one-carbon (1C) metabolism. This is important because it affects many key processes in the cell, including DNA synthesis, DNA methylation and cell proliferation. It does this by delivering methyl groups, which are central to these biochemical reactions. Deficiencies in metabolites involved in these pathways, such as choline, methionine, folate and vitamin B12, have adverse effects on animal development and wellbeing. For example, deficiencies in vitamin B12 and/or folate can affect fertility and fetal development, and lead to poor growth, vascular disease and metabolic syndrome in adult animals and humans. 1C metabolism pathways are complex and are affected by many genes. We hypothesise that mutations in these genes will affect 1C metabolism and the vulnerability of animals to micronutrient deficiencies. In this study we will identify such mutations, determine their functional significance (i.e. what they do and how important they are), test their impact in animals fed different diets, and find ways to use this information to improve the welfare of farm animals.Firstly, we will identify mutations (i.e. single nucleotide polymorphisms or SNPs) in around 40 genes directly affecting 1C metabolism, and in very closely related pathways involved in energy metabolism, cell proliferation, DNA synthesis and DNA methylation. To achieve this in sheep we will create our own sequence data. We estimate that we will identify 2000-4000 SNPs by these methods. We will then conduct a large-scale study with liver samples collected from around 300 sheep slaughtered at local abattoirs. We will genotype each sample (to determine which SNPs are present), measure gene expression and conduct a comprehensive analysis of all metabolites involved in 1C metabolism. Interpretation of these data will inform us on SNP function and how these SNPs affect pathways involved in 1C metabolism. To achieve this we will collate the required information and, using our knowledge of these genomes combined with complex bioinformatic analyses, determine the subset of SNPs that have the greatest impact on 1C metabolism. We expect to identify an estimated 100 or so functionally significant SNPs in these genes. We will then construct a 'SNP chip'; i.e. a tool to genotype sheep simultaneously and cheaply for many SNPs. This chip will be used to screen several flocks of sheep to identify 24 'Low-risk' and 24 'High-risk' weaned lambs, and 24 'Low-risk' and 24 'High-risk' breeding ewes. We will then monitor these animals in separate studies involving Control and Methyl-Deficient diets (i.e. two genotypes by two diets). For weaned lambs we will focus on effects on growth, animal health and liver metabolism, and carcass yields and composition. For breeding ewes we will also focus on animal health and liver metabolism, but extend studies to consider effects on chemical modifications to DNA (i.e. DNA methylation) in early (Day 16) male and female embryos. This research will provide novel insights into nutrient x gene interactions for many components of 1C metabolism and how they affect (a) lamb production efficiency, health and welfare, and (b) early development of mammalian embryos influencing fertility and the long-term health and wellbeing of offspring. We will be able to use this information to help breed animals with better functioning 1C metabolism (leading to permanent improvements in welfare and productivity) and/or to improve animal diets. As 1C metabolism also influences human development and health our results will also have biomedical research benefits, and increase the utility of sheep as a model species for this type of research.